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Joseph Aicher  |  PhD Student  |


I grew up in Colorado and studied at Alabama for four years before moving to Philadelphia to pursue MD-PhD training at Penn. Over the years, I have had the opportunity to work on research projects and develop skills in a variety of biomedical and computational disciplines that have motivated and reinforced my career goals of becoming an interdisciplinary physician scientist. As a high-school senior, I did research in applied mathematics at CU Boulder and medical genetics at Children’s Hospital Colorado. As a college student, I studied mathematics and physics and did computational and quantitative research at Alabama and UNC Chapel Hill. Much of this work was interdisciplinary in nature and combined the expertise of biologists, computer scientists, physicists, and mathematicians to address fundamental problems in biology. In 2015, I completed my master’s thesis in mathematics investigating the application of probabilistic graphical models to metabolomics data under the supervision of my master’s thesis advisors Drs. Laura Reed and Song Song.

I have been a student at Penn since then. I joined Dr. Yoseph Barash’s lab in 2018 and am co-mentored by Dr. Elizabeth Bhoj at the Children’s Hospital of Philadelphia. Scientifically, I am interested in machine learning, statistical modeling, genomics, and biomedical informatics, especially as they relate to human health. In particular, I am interested in the development and application of new computational tools and frameworks for understanding and predicting biological processes relevant to disease. My current work focuses on extending the lab’s deep learning models for predicting changes in splicing to better reflect the impact of genetic variants and applying these models to identify disease-causing variants in children with multiple congenital anomalies and other suspected Mendelian disorders.

  • Machine learning

  • Computational biology

  • Biomedical informatics

  • Alternative splicing

  • Genetic variations and genomics of human disease


Lawrimore J, Aicher JK, Hahn P, Fulp A, Kompa B, Vicci L, Falvo M, Taylor RM, Bloom K. ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin. Mol Biol Cell. 2016 Jan 1;27(1):153–166.


Aicher JK. Metabolic network inference with the graphical lasso [master’s thesis]. [Tuscaloosa (AL)]: University of Alabama; 2015. 31 p.


Baker PR, Friederich MW, Swanson MA, Shaikh T, Bhattacharya K, Scharer GH, Aicher J, Creadon-Swindell G, Geiger E, MacLean KN, Lee W-T, Deshpande C, Freckmann M-L, Shih L-Y, Wasserstein M, Rasmussen MB, Lund AM, Procopis P, Cameron JM, Robinson BH, Brown GK, Brown RM, Compton AG, Dieckmann CL, Collard R, Coughlin CR, Spector E, Wempe MF, Van Hove JLK. Variant non ketotic hyperglycinemia is caused by mutations in LIAS, BOLA3 and the novel gene GLRX5. Brain. 2014 Feb;137(2):366–379.

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